MolNFT v1 · #105850 · DNA

DNA duplex with novel zp base pair

4RHD · DNA 9MER novel Z nucleobase: “DNA duplex with novel zp base pair”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.27). MolNFT v1 #105850 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4RHD
Type: DNA
Length: 72 nucleotides
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA 9MER novel Z nucleobase
Ligands: MG
Pockets: 4 · best druggability 0.27

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	DNA 9MER novel Z nucleobase	dna	9	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, C, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	73	0.27	0.73	9	empty
2	71	0.27	0.72	10	empty
3	65	0.26	0.73	13	empty
4	67	0.25	0.72	11	empty

Interfaces

8 interfaces between chains.

E–F · 425 Å² buried · 44 hydrogen bonds · nucleic-nucleic
A–B · 417 Å² buried · 43 hydrogen bonds · nucleic-nucleic
C–D · 416 Å² buried · 37 hydrogen bonds · nucleic-nucleic
G–H · 413 Å² buried · 40 hydrogen bonds · nucleic-nucleic
B–H · 104 Å² buried · 7 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 16 modified (nucleotide modification).

Compared structures

4RHD · DNA Duplex with Novel ZP Base Pair · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 4RHD · PDBe 4RHD

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.